Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals
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Publication Date: | 2021 |
Other Authors: | , , , , , , , , , |
Format: | Article |
Language: | eng |
Source: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Download full: | http://hdl.handle.net/10451/59028 |
Summary: | Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. The resulting assembled chromosomes were between 5.2 and 5.5Mbp in length, and twenty-six PEGEs were found. Four of our eight samples carry blaCTX-M-15, a dominant Extended Spectrum Beta Lactamase in Europe. We identified methylation motifs that control Restriction–Modification systems, including GATC of the DNA adenine methylase (Dam), which methylates N6-methyladenine (m6A) across all our K. pneumoniae assemblies. There was a consistent lack of methylation by Dam of the GATC motif downstream of two genes: fosA, a locus associated with low level fosfomycin resistance, and tnpB transposase on IncFIB(K) plasmids. Overall, we have constructed eight high quality reference genomes of K. pneumoniae, with insights into horizontal gene transfer and methylation m6A motifs. |
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Methylation analysis of Klebsiella pneumoniae from Portuguese hospitalsKlebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. The resulting assembled chromosomes were between 5.2 and 5.5Mbp in length, and twenty-six PEGEs were found. Four of our eight samples carry blaCTX-M-15, a dominant Extended Spectrum Beta Lactamase in Europe. We identified methylation motifs that control Restriction–Modification systems, including GATC of the DNA adenine methylase (Dam), which methylates N6-methyladenine (m6A) across all our K. pneumoniae assemblies. There was a consistent lack of methylation by Dam of the GATC motif downstream of two genes: fosA, a locus associated with low level fosfomycin resistance, and tnpB transposase on IncFIB(K) plasmids. Overall, we have constructed eight high quality reference genomes of K. pneumoniae, with insights into horizontal gene transfer and methylation m6A motifs.S.C. is funded by Bloomsbury SET, Medical Research Council UK (MR/M01360X/1, MR/R025576/1, and MR/R020973/1) and BBSRC (Grant No. BB/R013063/1) grants. T.G.C. is funded by the Medical Research Council UK (Grant Nos. MR/M01360X/1, MR/N010469/1, MR/R025576/1, and MR/R020973/1) and BBSRC UK (Grant No. BB/R013063/1). This study was supported in part by UID/DTP/04138/2019 from Fundação para a Ciência e Tecnologia (FCT), Portugal. J.Pe. is supported by FCT through Estímulo Individual ao Emprego Científico (CEECIND/00394/2017).Springer NatureRepositório da Universidade de LisboaSpadar, AntonPerdigão, JoãoPhelan, JodyCharleston, JamesModesto, AnaElias, RitaDe Sessions, PaolaHibberd, Martin L.Campino, SusanaDuarte, AidaClark, Taane G.2023-08-25T16:20:05Z2021-03-222023-03-13T20:30:45Z2021-03-22T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/59028engpadar A, Perdigão J, Phelan J, Charleston J, Modesto A, Elias R, et al. Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals. Sci Rep [Internet]. 22 de março de 2021;11(1):6491. Disponível em: https://www.nature.com/articles/s41598-021-85724-22045-2322cv-prod-285384310.1038/s41598-021-85724-2info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T17:04:29Zoai:repositorio.ul.pt:10451/59028Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:07:12.684102Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals |
title |
Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals |
spellingShingle |
Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals Spadar, Anton |
title_short |
Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals |
title_full |
Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals |
title_fullStr |
Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals |
title_full_unstemmed |
Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals |
title_sort |
Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals |
author |
Spadar, Anton |
author_facet |
Spadar, Anton Perdigão, João Phelan, Jody Charleston, James Modesto, Ana Elias, Rita De Sessions, Paola Hibberd, Martin L. Campino, Susana Duarte, Aida Clark, Taane G. |
author_role |
author |
author2 |
Perdigão, João Phelan, Jody Charleston, James Modesto, Ana Elias, Rita De Sessions, Paola Hibberd, Martin L. Campino, Susana Duarte, Aida Clark, Taane G. |
author2_role |
author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Repositório da Universidade de Lisboa |
dc.contributor.author.fl_str_mv |
Spadar, Anton Perdigão, João Phelan, Jody Charleston, James Modesto, Ana Elias, Rita De Sessions, Paola Hibberd, Martin L. Campino, Susana Duarte, Aida Clark, Taane G. |
description |
Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. The resulting assembled chromosomes were between 5.2 and 5.5Mbp in length, and twenty-six PEGEs were found. Four of our eight samples carry blaCTX-M-15, a dominant Extended Spectrum Beta Lactamase in Europe. We identified methylation motifs that control Restriction–Modification systems, including GATC of the DNA adenine methylase (Dam), which methylates N6-methyladenine (m6A) across all our K. pneumoniae assemblies. There was a consistent lack of methylation by Dam of the GATC motif downstream of two genes: fosA, a locus associated with low level fosfomycin resistance, and tnpB transposase on IncFIB(K) plasmids. Overall, we have constructed eight high quality reference genomes of K. pneumoniae, with insights into horizontal gene transfer and methylation m6A motifs. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-03-22 2021-03-22T00:00:00Z 2023-08-25T16:20:05Z 2023-03-13T20:30:45Z |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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http://hdl.handle.net/10451/59028 |
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http://hdl.handle.net/10451/59028 |
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eng |
language |
eng |
dc.relation.none.fl_str_mv |
padar A, Perdigão J, Phelan J, Charleston J, Modesto A, Elias R, et al. Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals. Sci Rep [Internet]. 22 de março de 2021;11(1):6491. Disponível em: https://www.nature.com/articles/s41598-021-85724-2 2045-2322 cv-prod-2853843 10.1038/s41598-021-85724-2 |
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info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Springer Nature |
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Springer Nature |
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